Genomic and Bioinformatic Resources for Perennial Fruit Species

In the post-genomic era, data management and development of bioinformatic tools are critical for the adequate exploitation of genomics data. In this review, we address the actual situation for the subset of crops represented by the perennial fruit species. The agronomical singularity of these species compared to plant and crop model species provides significant challenges on the implementation of good practices generally not addressed in other species. Studies are usually performed over several years in non-controlled environments, usage of rootstock is common, and breeders heavily relies on vegetative propagation. A reference genome is now available for all the major species as well as many members of the economically important genera for breeding purposes. Development of pangenome for these species is beginning to gain momentum which will require a substantial effort in term of bioinformatic tool development. The available tools for genome annotation and functional analysis will also be presented.Publishe

Génomique fonctionnelle et marqueurs de qualité chez l'abricot

En lien avec la sélection assistée par marqueurs de la qualité des fruits chez l'abricotier (Prunus armeniaca), 71 marqueurs moléculaires impliqués dans la régulation hormonale et dans le contrôle de l'acidité, du taux de sucre, de la texture, de la biosynthèse des arômes, et des pigments, ont été mis en évidence par étude conjointe de l'évolution du transcriptome et du protéome au cours de la maturation et entre génotypes contrastés. Une base de données a été construite contenant 5200 unigènes formés à partir de 18000 EST, fonctionnellement annotés et regroupés par familles multigèniques. Des lames de microarray ont été construites sur lesquelles 1800 unigènes pertinents ont été déposés sous forme d'oligonucléotides 50 mères définis dans la région 3' non codante des transcrits. Celles-ci ont permis de mener l'étude de l'expression des gènes au cours du développement de la variété Bergeron et au travers différentes variétés contrastées pour la vitesse de maturation, la production d'éthylène et la couleur. L'évolution de l'abondance des protéines totales de Bergeron a été étudiée au cours de son développement par électrophorèse bidimensionnelle. Pour faciliter l'identification des spots protéiques, une base de données de protéines végétales chimériques incluant les mutations spécifiques du genre Prunus au sein des séquences complètes de leurs meilleurs orthologues à été construite à partir des données EST. ABSTRACT : In order to improve apricot (Prunus armeniaca) quality with markers assisted selection, 71 molecular markers involved in hormonal regulation and control of acidity and sugar content, texture, flavours and pigments biosynthesis were highlighted by transcriptomics and proteomics comparison of ripening stages and contrasted genotypes. Thus a database, containing 5200 unigenes extracted from 18000 functionally annotated and multigenic families gathered EST, was designed. Microarrays slides were built, and 1800 relevant unigenes were spotted as specific 50mers oligonucleotides designed in the 3' untranslated region of transcripts. Gene expression study was performed on Bergeron cultivar development and between contrasted cultivars for ethylene outburst and color. Total proteins abundance during Bergeron development was analyzed on two-dimensional gel electrophoresis. For improving identification, a plant proteins database including mutations from conceptually translated expressed sequence tags from Prunus into best matches, was designed

Proteomic analysis of shoot tissue during photoperiod induced growth cessation in V. riparia Michx. grapevines

<p>Abstract</p> <p>Background</p> <p>Growth cessation, cold acclimation and dormancy induction in grapevines and other woody perennial plants native to temperate continental climates is frequently triggered by short photoperiods. The early induction of these processes by photoperiod promotes winter survival of grapevines in cold temperate zones. Examining the molecular processes, in particular the proteomic changes in the shoot, will provide greater insight into the signaling cascade that initiates growth cessation and dormancy induction. To begin understanding transduction of the photoperiod signal, <it>Vitis riparia </it>Michx. grapevines that had grown for 35 days in long photoperiod (long day, LD, 15 h) were subjected to either a continued LD or a short photoperiod (short day, SD, 13 h) treatment. Shoot tips (4-node shoot terminals) were collected from each treatment at 7 and 28 days of LD and SD for proteomic analysis via two-dimensional (2D) gel electrophoresis.</p> <p>Results</p> <p>Protein profiles were characterized in <it>V. riparia </it>shoot tips during active growth or SD induced growth cessation to examine physiological alterations in response to differential photoperiod treatments. A total of 1054 protein spots were present on the 2D gels. Among the 1054 proteins, 216 showed differential abundance between LD and SD (≥ two-fold ratio, p-value ≤ 0.05). After 7 days, 39 protein spots were more abundant in LD and 30 were more abundant in SD. After 28 days, 93 protein spots were more abundant in LD and 54 were more abundant in SD. MS/MS spectrometry was performed to determine the functions of the differentially abundant proteins.</p> <p>Conclusions</p> <p>The proteomics analysis uncovered a portion of the signal transduction involved in <it>V. riparia </it>grapevine growth cessation and dormancy induction. Different enzymes of the Calvin-Benson cycle and glutamate synthetase isoforms were more abundant either in LD or SD treatments. In LD tissues the significantly differentially more abundant proteins included flavonoid biosynthesis and polyphenol enzymes, cinnamyl alcohol dehydrogenase, and TCP-1 complexes. In the SD tissue photorespiratory proteins were more abundant than in the LD. The significantly differentially more abundant proteins in SD were involved in ascorbate biosynthesis, photosystem II and photosystem I subunits, light harvesting complexes, and carboxylation enzymes.</p

Análisis de asociación (GWAS) para la fecha de cosecha y caracteres de calidad en el programa de mejora genética de "Melocotón de Calanda" del CITA

Melocotón de CalandaPublishe

Descifrar el genoma del Melocotón de Calanda para la preservación de la calidad de frutos

Melocotón de Caland

Programa de mejora genética del melocotón de Calanda

Financiado por Gobierno de Aragón, a través del Fondo de Inversiones de Teruel (años 2019 y 2020), con la participación del Gobierno de España (Ministerio de Política Territorial)Melocotón de Caland

Análisis de genes candidatos en el QTL principal de periodo y fecha de maduración en cerezo

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Network of GRAS transcription factors in plant development, fruit ripening and stress responses

The plant-specific family of GRAS transcription factors has been wide implicated in the regulation of transcriptional reprogramming associated with a diversity of biological functions ranging from plant development processes to stress responses. Functional analyses of GRAS transcription factors supported by in silico structural and comparative analyses are emerging and clarifying the regulatory networks associated with their biological roles. In this review, a detailed analysis of GRAS proteins' structure and biochemical features as revealed by recent discoveries indicated how these characteristics may impact subcellular location, molecular mechanisms, and function. Nomenclature issues associated with GRAS classification into different subfamilies in diverse plant species even in the presence of robust genomic resources are discussed, in particular how it affects assumptions of biological function. Insights into the mechanisms driving evolution of this gene family and how genetic and epigenetic regulation of GRAS contributes to subfunctionalization are provided. Finally, this review debates challenges and future perspectives on the application of this complex but promising gene family for crop improvement to cope with challenges of environmental transition

Deciphering the molecular mechanisms behind essential oil treatement against downy mildew in grapevine

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